Skepticism

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Graaarh, physicistsBIOLOGISTS

I thought physics was the most hubristic scientific discipline of them all, but I may have to revise that assessment. Last week I was sent another of those papers published in archiv, the physics repository, making grand pronouncements about evolution, and I made the mistake of simply dismissing it on twitter — it was simply too ridiculous to post about. But now io9 has picked it up, and more people are clamoring at me to explain it.

An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant functional nucleotides, is expected to have grown exponentially due to several positive feedback factors: gene cooperation, duplication of genes with their subsequent specialization, and emergence of novel functional niches associated with existing genes. Linear regression of genetic complexity on a log scale extrapolated back to just one base pair suggests the time of the origin of life 9.7 billion years ago. This cosmic time scale for the evolution of life has important consequences: life took ca. 5 billion years to reach the complexity of bacteria; the environments in which life originated and evolved to the prokaryote stage may have been quite different from those envisaged on Earth; there was no intelligent life in our universe prior to the origin of Earth, thus Earth could not have been deliberately seeded with life by intelligent aliens; Earth was seeded by panspermia; experimental replication of the origin of life from scratch may have to emulate many cumulative rare events; and the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe. Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet. As a result the doubling time of complexity has reached ca. 20 years. Finally, we discuss the issue of the predicted technological singularity and give a biosemiotics perspective on the increase of complexity.

Life originated 9.7 billion years ago, huh? Maybe 13 billion plus years ago? I didn’t even have to read the paper: I predicted that there would be a certain graph in it, opened it up, scanned to Figure 1, and there it was.

We’re done. Anyone else see the problem?

They cherrypicked their data points. They didn’t include lungfish, ferns, onions, or some protists because that would totally undermine their premise; those are contemporary organisms with much larger genomes than mammals’, and their shallow, stupid exercise in curve-fitting would have flopped miserably. It’s a great example of garbage in, garbage out.

There’s another figure, in which they slap their ‘origin of life’ numbers on a diagram of the history of the universe. Very convincing. I could also stick a label on such an image and show the ‘origin of clowns’ at the time of the Big Bang. It wouldn’t make it scientific, though.

Do they have any other evidence to support their claim? No, not one bit. Most of the paper is a handwavey summary of various models of abiogenesis, with no effort to be quantitative…except for their quantitative claim on the basis of one fudged graph that life originated over 9 billion years ago. There’s also some weird stuff about biosemiotics, which they use to argue for goals and meaning in evolution. It seems to be a popular term among creationists, and what little I’ve read on it from marginally more credible sources makes it look like nonsense.

That graph, though, just kills it. At least try to respect the larger data set, will ya, guys?

This was published in archiv, probably to escape the restrictions of peer review (i.e., slip some bullshit under the door), and really, I read that and thought, “physicists, again?” But then I looked closer at the authors. I am so ashamed.

Don’t forget fugu! Kills their data point the other way. Although it looks like they’re doing their regression based on “functional, non-redundant genome”, so depending on how that is interpreted, they may already have lungfish and stuff in there and just classified all the extra genome as “junk” and didn’t count it.

I am not in any sense a biologist (my interests lay mainly in electronic gadgetry), so I am not qualified to determine the validity of their method, however some other things that should be wondered about:

For the data points on there, they’d have to be using modern genome sizes for the various milestones since I don’t think there’s any way in hell the genome of an ancient prokaryote has been preserved. I’ve read enough on evolution (mostly Dawkins and Coyne) that I don’t need it explained to me why this is stupid. These guys are PhD biologists and can’t even see that?

However, now I recall all the people I’ve met (presumably) educated in electronics arguing about why vinyl is better than CDs because “analog is an exact replica of the original signal and digital loses information”, and I deeply feel your embarrassment.

Anyone seriously making such far reaching and world changing conclusions based on a linear regression of cherry picked data AND NOTHING ELSE needs to be slapped with their own diploma.

They didn’t include lungfish, ferns, onions, or some protists because that would totally undermine their premise; those are contemporary organisms with much larger genomes than mammals’, and their shallow, stupid exercise in curve-fitting would have flopped miserably. It’s a great example of garbage in, garbage out.

Maybe I’ve been out of labs way, way too long, but I need help on this one. If one included lungfish, ferns, onions and a few protists, what does the chart look like?

Lets see remembering back from my invertebrate zoology days (great class got to TA the lab too ^.^ ) we have flat worms, round worms, annelids, horse hair worms, velvet worms, acorn worms just off the top of my head. All very different distinct phylum of animals (humans and fish would be more closely related then those groups). So what on earth did they mean by “worms”?

I looked at his CV. Sharov is also a “theoretical biologist”. I prefer to read that as “theoretically, a biologist”.

If a more reasonably diverse selection of organisms were included, mammals would be unexceptionally buried in the middle of a collection of data points, some many times bigger, others many times smaller. Prokaryotes and eukaryotes are still extant, obviously, so those two data points would have to expand to a messy two-dimensional smear. The entire premise of imposing a linear plot on the data would be exposed as complete bullshit.

If we also want to poke at the “biosemiotics” side of it — I’ll have to take another look later, but at first glance it looks like it’s garbage in terms of semiotics as well as in terms of biology. It’s like somebody saw the word “semiotics” attached to the word “meaning” and decided that it would be a wonderful word to attach to their system of doctrines based on how biological phenomena have inherent “meanings” as a definable communication system (just like languages and other sign systems!). Of course, the fundamental messiness of semiosis wouldn’t suit their purposes well, so…

(On the other hand, the semiotic model in which there isn’t any solid definable “meaning”, but on the contrary a constant potential for varied interpretations of any given sign or set of signs by all parties…that could potentially mesh more productively with the messiness of biology on all levels from molecular to planetwide, complete with transcription errors and the like, through odd instances of coevolution, to human habits of making grand patterns out of samples of convenience. Hm…where could we find an example of that last bit…)

I almost discovered the same thing! (Soon to be published in a prestigious non-peer-reviewed journal.)

Consider:

1) The average height of a newborn baby is 17 inches.
2) The average height of an American adult man (21 years old) is 70 inches.

From birth to the age of 21 the average American man grows 53 inches, which equates to 0.21 inches per month.

THEREFORE, using a linear regression, we can show that for the baby to be 17 inches at birth he must have been growing for 80.83 months, which is a whopping 71.83 months before conception! LIFE BEGINS BEFORE CONCEPTION!

FWIW, the x-values of the points plotted aren’t the entire lifespan of the clade, they’re the estimated origin date for the clade. Good thing too since they are using genomic data; extinct taxa are hard to sequence.

There is no excuse for “prokaryotes” and “worms” though, nor for excluding plants and fungi.

Crip Dyke, Right Reverend Feminist FuckToy of Death & Her Handmaidensays

Also, apropos of nothing save discussing soft-bodied invertebrates, one of the girls was running around naked the other day, being happy & (at least metaphorically) colorful. I asked her if she was the “nudie branch” of the family.

If a more reasonably diverse selection of organisms were included, mammals would be unexceptionally buried in the middle of a collection of data points, some many times bigger, others many times smaller. Prokaryotes and eukaryotes are still extant, obviously, so those two data points would have to expand to a messy two-dimensional smear. The entire premise of imposing a linear plot on the data would be exposed as complete bullshit.

Actually, that might be interesting to see. Does someone has enough data to plot out the genome size versus time of origin for as much organisms as they could get?

Also, why is the graph couched in terms of greatest similarity to humans? Looks like some teleological scala naturae hidden in their teleological background. Talking strictly butterflies, did I mention the 6,000+ species of Lycaenid+ Riodinid have mitochondrial genomes about as large as humans. The 6,000 species of Nymphalidae, ditto. This is 2x the number of species of mammals. Some noctuid moths have mitochondrial genome sizes more than 25% larger than humans. Results from CO1 gene and a quick google scholar searchs. Why is this graph anything like a straight line even on a log scale?

The strange thing about biosemiotics is that they have a peer-rewieved journal published by a well respected publisher, and a lot of philosophers at real well respected universities seem to be involved in the field.

Hey, it isn’t just biology that these guys can mess up — they also don’t understand even the popularized version of astronomy. Don’t forget

the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe

First of all, unless these guys have been involved in astral travel between the various galaxies, how the heck do they know this for sure? And secondly, if they understood the Drake equation even slightly, they’d know that of the seven variables it contains, we only have data for the first three of them. So right now, depending on what variables you pull out of thin air to apply to the last four, you could conclude that intelligent life is incredibly rare or incredibly common. But you can’t say the equation itself is wrong, since it makes no attempt to fill in the variables — the only real grounds you’d have to criticize it would be if you said there was some other variable that it left out.

Great Chain of Being, Batman!
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There is no genetic, let alone genomic, data older than ~ 50,000 years. So they are substituting modern worms and fish for prehistoric versions.
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And that’s a long way to extend your fitted line, 9 billion years from data of less than 50,000 years.

[BTW been a long while since I’ve seen your monicker – just missing each other or were you gone & back?]

I don’t think that theoretical biologist *can* be the same thing. Physics is so reducible to numbers, that you can put the numbers together any way you want. Biology is different. No one measure the “output”, so to speak, of a new species and then builds a mathematical model to predict the form of an enzyme used in digestion. Part of this is that it’s just easy to sample the enzyme. Part is that there are so many chemical precursors to large bio-molecules that there are also a number of reasonable pathways to get there, and even more enzymes that might or might not play a role, and then to get the exact output would depend not merely on the input and the enzyme, but the body temp, the length of the digestive system, etc. etc.

Ultimately, it comes down to the fact that biology is overdetermined. There are so many possible factors, and the presence of one changes the odds of the presence of another. How could we predict, theoretically, which were in play and which weren’t?

Physics you have 4 fundamental forces…and that’s it. In many cases one or more of them don’t even play a role in whatever mystery is being investigated. So educated guesses are much more likely to be right, b/c there are fewer ways to be wrong.

Also, the hypothesis is what is used to construct experiments. Once you have a theory, you can use it to hypothesize about certain predictions, which leads to specific experiments. That’s often useful when you’re proposing experiments that cost billions, to make sure you get useful answers. A zebra fish doesn’t cost billions, so that’s a different thing, too.

Anyway, yes, theory plays a role in biology. No, I don’t think there’s anything comparable to “theoretical physics” in biology.

Generally speaking, one of the first things one does when working over multivariate quantitative data is to plot one variable against another and if there are signs of correlation, jam a straight line through the points using ordinary least squares. It’s a perfectly reasonable, perfectly valid thing to do when you have good data.

But these idjits don’t have good data at all. They should be ashamed of themselves for foisting such nonsense on the world. For example, an alternative analysis of this graph concludes that the longer a taxon exists, the smaller its genome. “Genome shrinkage”, we can call it. You read it here first.

But that conclusion is no more valid than the spurious nonsense one the authors came up with. What I smell here is someone’s discovery that they can do simple least squares analysis in spreadsheets, a facility that has been in place for decades now.

Let me suggest that Pharyngula readers who are professional biologists write the head of the NIH and point out that this paper, publilshed without peer review, besmirches the NIH’s reputation. It would be reasonable for the NIH to require that staff members who want to publish nonsense in unreviewed journals not mention their connection to NIH and do it strictly as private citizens. Or such other protocols as would prevent the NIH’s good name from being associated with pernicious nonsense.

There’s yet another point to be made, having now read Crip Dyke’s preceding remarks: the field of theoretical physics is founded on the amazing fact that the universe in many respects follows mathematical formulas, just why no one knows.

While in theory one can reduce biology to a branch of physics and then ride the coat tails of that amazing fact, in practice living organisms are far too complex for a mathematical approach to yield much insight into fundamentals. Certainly the question, “why do organisms have genomes of the size they do?” is a legitimate one, but this analysis falls flat on its face in relation to that question.

Well hmm, I’ve been lurking about for years now, and have often wondered when biosemiotics would show up on PZ’s radar, and I gotta say that it sucks that it comes with a reference to Sharov. The closest thing I had seen previous to this was one post several years ago where PZ referenced Brian Goodwin’s semiotic approach to biology with some mix of respect and dismissal (if I remember rightly, he called it a fascinating approach that ought not be cavalierly dismissed, but one that ultimately fails). But now, on the basis of what certainly looks like an absurd article and a 2 second google search, he rejects all of biosemiotics as nonsense.

First, I’ve met Sharov and read some of his papers. His background and interest seems to lie at the intersection of biology and statistics. As with many who work with theoretical biology and biosemiotics (including Marcello Barbieri, editor of the journal of biosemiotics), he is not much interested in ‘interpretive’ semiotics (and questions of ‘meaning’), but in codes, coding, code making – and the intersection of codes and information. Some would call what he does bioinformatics. He cut his teeth studying insects, in terms of populations as well as genetics, but my impression is that he was always far more comfortable crunching numbers than chitinous exoskeletons. While I will not (cannot) defend the paper that PZ (rightly) flags as absurd, I will say that this has no bearing on the work that others have done on the importance of semiotics in biology.

Second, the fact that some creationists use the same term says nothing about biosemiotics. Guilt by association is a tactic common to creationists and other religious anti science types, and is unworthy of PZ. After all, the discovery institute, et. al. are constantly talking about ‘evolution’ – and make a point of only dismissing ‘macro evolution’ while accepting ‘micro evolution.’ So should we stop studying evolutionary biology only because the term gets used by idiots who deliberately and maliciously twist its meaning? Should we dismiss evolution because those idiots use the term? To the contrary, PZ’s snark on creationists using the term ‘biosemiotics’ is a pointless non-sequitor.

Third, another favorite tactic of christian dominionists is to pick out some minor player from US history, over-rate his importance, emphasize his Xtianity, and claim that his existence is proof that the US government was never intended to be secular. So go ahead and dismiss this article. But don’t confuse it with something it isn’t. Don’t fall into the fallacy of dismissing the secular history of the US based on the ‘in gawd we trust’ printed on US money.

Third.2 reading something from the principles of the field is more useful than scanning Wikipedia. For those with a greater interest in the confluence of evolutionary biology and neural development, Terence Deacon’s The Symbolic Species is a wonderful read. If your thing is molecular biology, I advise you to turn to Barbieri, The Organic Codes. For developmental biology, Anton Markos’ Readers of the Book of Life is worth reading. For a more Darwinian (i.e., the evolution of populations) approach peppered with ‘interpretive’ biology, I would give you Jesper Hoffmeyer’s Signs of Meaning in the Universe. Also, while he doesn’t use the term ‘biosemiotic’, Stuart Kauffman’s theoretical biology is largely semiotic, and his work At Home in the Universe is largely a biosemiotic work. And as general reading in semiotic biology, I think that Barbieri has edited some excellent collections of essays, especially Biosemiotics: Information, Codes and Signs in Living Systems, I would also recommend Don Favareau’s Essential Reading in Biosemiotics. And finally, I cannot list the more important books of biosemiotics without referencing Sebeok’s The Play of Musement – it’s a great read, but frankly more interested in philosophy than biology.

Fourth, how the f@#$ do I write a list of good reads on an obscure subject without running afoul of the courtier’s reply?? I do not intend to claim that no one can possibly know anything until they have read these books, only that if you want to know something about biosemiotics, then you need to read something about biosemiotics. Scanning one sad article and a page on wikipedia doesn’t cut it. There is no great all encompassing gnosis, no ‘deeeeep’ knowing to the field. I know that PZ has already read Goodwin, and is likely to have read Deacon (though perhaps without realizing that he is part of the cohort), and so he damn well ought to be able to come to terms with biosemiotics – even if he ultimately dismisses it in favor of the classic neo-darwinian synthesis. But no, this is a relatively obscure, relatively young, and clearly theoretical approach to the study of biological systems; it is not courtier’s babbling, not creationist nonsense, and not limited to what Sharov wrote in the silly paper at the top of this thread. It is largely empirical and falsifiable (with the obvious exception of the silly paper at the top of this thread)

Finally, full disclosure: I have attended any number of biosemiotic conferences, review papers for the Journal of Biosemiotics, and have published a few of my own in the journal as well as other sources. My background is history and philosophy of science and my dissertation focused Peirce’s reading of Darwin. I am not a biologist, and do not play one on TV, however I do know how to read biology. To complete my studies, I had to pass any number of graduate level exams as well put my time in the labs. I generally recognize woo when I see it (at least in politics and biology – I am not qualified to discuss quantum woo). And I have seen it in biosemiotic conferences and journal submissions, but it is important to recall that woo is neither unique nor ubiquitous to biosemiotics.
tak, tecka, a dost.

So in physics we always seem to have a problem with people we call crackpots trying to present their theories at conferences. Most physics conferences create a parallel session called “General Physics” and move the talks whose abstract looks like crackpot to that session. For some reason all the crackpots don’t seem to mind and happily present their talks at the General Physics session to all the other crackpots.

If you will notice the paper is posted to the General Physics (physics.gen-ph) section of the arXiv. When you submit a paper to the arXiv, you have to say what section you want it in, physics.astro-ph is astrophysics phenomenology for example. When the editors of the arXiv see a paper that looks like a crackpot they change its section to General Physics rather than getting angry emails about how the self-appointed defenders of the orthodoxy are censoring them. So please don’t take any posting you find in General Physics to be any sort of indication of what physicists think (other than the authors of course.)

There’s a saying in academic circles, publish or perish. Hmmm, which was the worse option in this case?

I suppose one used to be able to publish to some obscure journal and get the cred for being published without too many people actually reading the paper, but those days are long gone. Nothing is too obscure for the great god Google, the all knowing and omnipresent one.

Richard Gordon, theoretical biologist, was born in New York in 1943, the eldest son of a salesmen and American handball champion[1] [Jack Gordon] and artist Diana Gordon. He was educated at University of Chicago where he did an undergraduate degree in Mathematics and then completed a PhD at University of Oregon in Chemical Physics under Terrell L Hill. Richard Gordon is best known for interdisciplinary and cross disciplinary work bridging biology and fields such as mathematics, engineering, physics and chemistry. He was a professor at the University of Manitoba, Winnipeg Canada 1978-2011. He recently retired and currently works as an emeritus scientist for the Gulf Specimen Marine Laboratory in Panacea Florida.

I’m a longtime lurker, first time posting, I even set up an ID and password just to comment.

I’m a professor of Environmental Science at Florida A&M University in Tallahassee, FL. The address of the second author is the Gulf Specimen Marine Lab, which is located in Panacea, FL, about 20 miles from here.

The Gulf Specimen Marine Lab is (or was?) a mom and pop operation that collected fish and invertebrates from the Gulf of Mexico for teaching and research purposes for the last 20 or 30 years. If you’ve read Steinbeck’s “Cannery Row”, think about Doc’s lab in Monterrey… It was run by Jack and Ann Rudloe, but Ann passed away last year. I believe (but am not sure) that their son now runs or manages the place. Website is http://www.gulfspecimen.org/

My department runs a summer camp for high school kids interested in marine biology, and we go there most every summer; they have some touch tanks and the kids get to handle live crabs, skates & such and explore salt marshes. This is not a research facility by any standards, although they may publish some notes about species distributions, reports of rare species in the area, etc. Mostly, they collect and sell stuff to schools, colleges, and the odd collector.

I don’t generally care where author’s primary affiliations are when I first look at a paper, because people who are not associated with big research centers or universities can certainly produce interesting and important science. Still….if you want to overturn decades of published stuff, you need damn good evidence and arguments. Clearly that’s missing here, and the institution that the author identifies himself with really lacks the intellectual horsepower you might expect to support of this kind of work.

geraldostdiek @ #33
“Fourth, how the f@#$ do I write a list of good reads on an obscure subject without running afoul of the courtier’s reply??”

The courtier’s reply is a situation where someone defends something factually wrong on the grounds that the discourse surrounding it is so valuable it renders its factual bankruptcy irrelevant. (which is not the same as saying merely that said discourse is valuable or interesting. Much of History would be thus if people couldn’t talk about the way people perceived their world in the past based on factually incorrect premises)
In this case I think you’d duck the problem by explaining what biosemiotics’ value is as a field, since you think people are misunderstanding it. If you think it is fact based and worthwhile, say how rather than saying mostly “it’s not as bad as it sounds and here’s some books I like”. No offense, but that’s what I got out of it.

What a load of crap. Not only PZ’s points, but they extrapolate their stupid line back to locate the origin of life, which they define as a single pair of nucleotides! It doesn’t get much stupider.

Crip Dyke @#28: you don’t know what you’re talking about.
Yes of course there is ‘theoretical biology’. Journals, departments, everything. Modern disciplines of ecology, evolutionary biology, and animal behavior are all about testing predictions from mathematical theory, for example.
Here, lmgtfy.

Question : why does the graph of development have to be linear ?

It’s not–those are semilog coordinates, so a straight line on that graph actually represents an exponential curve. They justify this in the abstract, handwavingly predicting an exponential increase because of various positive-feedback effects.

Thanks for the comment Muz; I quite agree. You describe my post unfortunately well, I will take your advice:

The central idea of biosemiotics is that living things go about living by ‘reading’ what ‘signs’ they are able to discern from the environment. A ‘sign’ is that thing that stands for another thing to some living thing; signs are not limited to abstract symbolic constructs, but co-exists with every ‘minding’ – signs are inferred within every interaction in which some living thing is seen to extract awareness of some feature of its surrounds. (E.g., an amoeba swimming up a glucose gradient or a human getting directions to Brno from a roadside placard.) This not only informs the actions of the living thing and its individual development, but also serves as a factor of selection and evolution. The argument is that biological mechanisms are semiotically realized. If this is true, then we can expect to learn something (not everything, something) about biological processes by isolating and identifying various sign functions (as best we can, semiosis, like biology, is messy, irrational, and driven by history and need). This is neither limited to, nor eliminated by human culture: in my view (Deacon would agree, Barbieri would not), biosemiotic function is the ‘missing link’ between abstracted human constructions and the rest of nature; it eliminates the need for the ill defined philosophical concept of epistemology by memetic replication. I know of no-one who thinks that biosemiotics simply replaces the neo-darwinian synthesis; the argument is that it complements it. In addition to serving to isolate some specific factors of evolutionary and developmental biology, it also allows for a useful extrapolation from biological processes to human experience.

Hey, I’m curious – what philosophers are you talking about, involved with the biosemiotics stuff? Most of the time I hear “semiotics” and “philosophy” mentioned in the same breath, it’s Continental philosophers that are being discussed, and of course, as I’ve noted elsewhere, what goes on in Continental departments is not only a poor representation of Anglophone philosophy but also in a distinct minority in the field. Mind you, the fact that the Pragmatists were also into semiotics (some of them, anyway, like Pierce) changes things a little, but Pragamatism is not exactly mainstream analytic, either.

There’s another figure, in which they slap their ‘origin of life’ numbers on a diagram of the history of the universe. Very convincing. I could also stick a label on such an image and show the ‘origin of clowns’ at the time of the Big Bang. It wouldn’t make it scientific, though.

Really? They put up a graph that prominently features the inflation phase next to their graph that presumes evolution has been the same ever since the beginning of life?

I thought it was a well-known fact that mutation rates are not similar among different organisms, and thus “molecular clocks” are misleading. Genome size must have some connection to mutations, so you have a problem right there. And I do not even have a degree in biology.